AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i002_bsub_mtub_300.orf -o002_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 deoD 300 purine nucleoside phosphorylase #2 drm 160 phosphodeoxyribomutase #3 ripX 300 integrase/recombinase #4 cdd 118 cytidine/deoxycytidine deaminase #5 yqfF 78 yqfF #6 yqfC 56 yqfC #7 yqfB 24 yqfB #8 yqfA 21 yqfA #9 yqeZ 130 yqeZ #10 rpsU 163 ribosomal protein S21 #11 yutK 136 similar to Na+/nucleoside cotransporter #12 yuzB 262 yuzB #13 pdp 29 pyrimidine-nucleoside phosphorylase #14 nupC 115 pyrimidine-nucleoside transport protein #15 dra 105 deoxyribose-phosphate aldolase #16 deoR 90 transcriptional regulator #17 yxxB 72 yxxB #18 yxeR 69 similar to ethanolamine transporter #19 yxeN 22 similar to amino acid ABC transporter (permease) #20 yxeM 24 similar to amino acid ABC transporter (binding protein) #21 yxeK 185 similar to monooxygenase #22 yxeI 154 similar to penicillin amidase #23 yxeH 39 similar to hypothetical proteins #24 yxeF 87 yxeF #25 Rv0475 300 hypothetical protein Rv0475 #26 Rv0476 111 hypothetical protein Rv0476 #27 cdd 236 cdd Motif number 1 CGCTCTAAACAAAAAAGCCGCAGCCACCTG 2 14 0 AAAAAAGCCG 0.797661 -147 GACGTATAGAAAAAAAGGAGGCTTTCAAG 2 142 1 AAAAAAGGAG 0.946714 -19 AGCATAATAGAACAAAGCGGTAAAACCGGT 3 131 0 AACAAAGCGG 0.576786 -170 GGATCAGGATGAAAAAGGCGGATGGTTCGA 3 240 1 GAAAAAGGCG 0.672049 -61 ATGGGCGTGAAAAAAAGCGCGCGATTATGT 4 49 1 AAAAAAGCGC 0.616857 -70 TGTGTATGATTTGAAAGGAGGTTCTAACAC 6 12 0 TTGAAAGGAG 0.423523 -45 TACACATGAGATGAAAGGGGGTTCTTTTTG 6 36 1 ATGAAAGGGG 0.88034 -21 ATGGCAAAGAAAAGGACATCTTTCTAA 9 8 1 AGAAAAGGAC 0.804149 -123 GGCACTTATTATAAAAGGAAGGAGGGATAC 9 104 1 ATAAAAGGAA 0.724071 -27 TATATAATGAAAGAAAGGGGTTG 10 4 0 AAGAAAGGGG 0.909198 -160 AGAAAAGGGCCTGGACAGGC 11 1 1 AGAAAAGGGC 0.81675 -136 ACGGCAAAATAAAAAAGGGCCTGTCCAGGC 11 19 0 AAAAAAGGGC 0.833089 -118 TACTCTTCGGATTAAAGGGGAATTCAA 12 8 0 ATTAAAGGGG 0.667437 -255 AGCGAATACAAATAAAGGAGAAACACAT 14 98 1 AATAAAGGAG 0.715611 -18 ATATCTTAACAAAAAAGGAAGTGTGCGAAG 15 85 1 AAAAAAGGAA 0.781252 -21 AATCAGGTGGATGAAAGCCGGCGCCAGCCT 16 12 1 ATGAAAGCCG 0.600612 -79 AGCCTGTATAATAAAAGCAAATCAAAAGCA 16 37 1 ATAAAAGCAA 0.45842 -54 TCATACGTTTGAAAAAGGAGAAAACC 18 54 1 GAAAAAGGAG 0.748683 -16 AAATAGAAAAGGCGGGAAAATCAA 20 5 1 AGAAAAGGCG 0.916061 -20 TAAAAACATGATAAAAGGAGTATCGCC 21 169 1 ATAAAAGGAG 0.928846 -17 TAATCTGAATTGAAAAGGGGACTGATCAA 22 136 1 TGAAAAGGGG 0.651183 -19 GCATTCGCCCAAAAAAGGAGGAAAGA 24 72 1 AAAAAAGGAG 0.946714 -16 GATGACGTGCAGCAAAGGAGACATGTAGTG 25 81 1 AGCAAAGGAG 0.776571 -220 AAAATAGTTAATGAAAGGAATACCC 25 286 1 ATGAAAGGAA 0.576703 -15 GGGCCGACTAAGAAAAGCCAGCCTAACCCC 27 196 0 AGAAAAGCCA 0.414398 -41 ********** Masking position 5 Map Score: 24.4159 Number of sites scoring better than the average of aligned sites = 1688 Number in coding regions = 1140 Number in noncoding regions = 548 Number of orfs with sites within 600 bp upstream = 600 Fraction of orfs with sites within 600 bp upstream = 0.0963701 Motif number 2 GTAAAAAAAGATCAACCGGTCGAACCATCCGCCTT 3 254 0 ACCCGTCGAC 0.936792 -47 TGCTGAATGACCCGATCGCCCGTTATCGGGT 5 7 1 AGCCGTCGCC 0.837609 -72 TCATTATATAGACAGGCAGTCGCACTCATGACGGA 10 24 1 GCGCATCGCC 0.993304 -140 AAAGCAGTCTGCCTTCCGTCAGCTCTTAATAGTTG 14 36 0 GCCCGCAGCC 0.964911 -80 TTATTATACAGGCTGGCGCCGGCTTTCATCCACCT 16 16 0 GCGCGCGGCT 0.820326 -75 TTGGCACAGTGGCACGCATTCGCCCAAAAAAGGAG 24 57 1 GCGCATCGCC 0.993329 -31 CGGCTGGATCAGCCTGCGGTCGACCTCACCCAGAT 25 15 0 ACGCGTCGAC 0.936791 -286 GGCTGATCCAGCCGATCGGCCGCGCTGGCCAACAG 25 36 1 GCTCGCCGCC 0.980281 -265 CTACGAACTCGACCGACAACCGACCCGACGATCAG 25 134 1 GCACACCGAC 0.858839 -167 TGGACGTTGGGGCAAGCGTCGGCTCCTCCAGGGAG 25 222 0 GCGCGCGGCC 0.986843 -79 AATCACCATCGACTCCGAGTCGCCCACGGGGCGAC 26 21 1 GCCGATCGCC 0.963967 -91 CCAACACGTCGACTCCGAGTCGCCCCGTGGGCGAC 26 39 0 GCCGATCGCC 0.963967 -73 GGTCCGAGGTGGCCGCCGCCCGCGCGAGACGGTTG 27 32 1 GCCCGCCGCC 0.997315 -205 AACAGCTAGAGCCGGGCAATCGAGCTTAACTTGGC 27 112 1 GCGCATCGAC 0.974749 -125 * * *** **** * Masking position 12 Map Score: 17.5695 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 305 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TTGTCAACGGGAATGAAAACGGTTTATACT 2 82 1 GAATGAAAAC 0.860041 -79 TCGCTAAGAGGTCTGACAACTCAAGTATAA 2 105 0 GTCTGACAAC 0.864214 -56 ATGGGAAGATTCCTGAAAACAGCTGTCGAT 3 77 1 TCCTGAAAAC 0.82947 -224 CCGGTAAACAGGATGAAAACTTTCAATGCA 3 106 0 GGATGAAAAC 0.975443 -195 TGAATCAAGAGTATGAAAACTATCATCGGT 3 171 1 GTATGAAAAC 0.915484 -130 AAATGGATCAGGATGAAAAAGGCGGATGGT 3 236 1 GGATGAAAAA 0.74027 -65 TGGCTGAAAATTCTTACATTT 4 2 1 GGCTGAAAAT 0.841239 -117 CTACAATTTAGCCTGAAAACACAAATTAGT 12 133 1 GCCTGAAAAC 0.986635 -130 AAATCAGGTGGATGAAAGCCGGCGCCAGC 16 10 1 GGATGAAAGC 0.872105 -81 GCATTATTCAGCCTAAAAACATGATAAAAG 21 156 1 GCCTAAAAAC 0.82947 -30 TGGGACTATAGCCTGAAAACGACATGAAGG 23 11 1 GCCTGAAAAC 0.986635 -29 GATCAGCTGGGCCTGACATCTACGAACTCG 25 115 1 GCCTGACATC 0.729901 -186 TCGACGTGTTGGATGCAAACCGCATAGTCT 26 62 1 GGATGCAAAC 0.86231 -50 ********** Masking position 8 Map Score: 11.9052 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 442 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 GTAAAATGGACGGGCTGGATGATAATTTAGA 1 262 1 CGGGCTGATG 0.95289 -39 CCGCAGGTGGCTGCGGCTTTTTT 2 3 1 GCAGGTGCTG 0.811786 -158 TACCAAAACGGGGAGTAGATCAAGA 3 286 1 GGGAGTGATC 0.777286 -15 TGATTGCTTATGGGCTTGATGTTTCAAGAGG 5 50 1 TGGGCTGATG 0.853247 -29 AAATCAGGTGGATGAAAGCCGGCG 16 4 1 TCAGGTGATG 0.739211 -87 GTCATCTGGGTGAGGTCGACCGCAGGCTGAT 25 12 1 TGAGGTGACC 0.823877 -289 GCGCGGCCGATCGGCTGGATCAGCCTGCGGT 25 30 0 TCGGCTGATC 0.620939 -271 ACGTCATCGACGGAGTCGCTGTTGGCCAGCG 25 58 0 CGGAGTGCTG 0.954241 -243 CTGACATCTACGAACTCGACCGACAACCGAC 25 127 1 CGAACTGACC 0.741247 -174 GACATGGCACGCGACTTGCCGGGGAAACCTT 25 169 0 GCGACTGCCG 0.662425 -132 GTGGGCGACTCGGAGTCGATGGTGATTCGGA 26 17 0 CGGAGTGATG 0.943025 -95 CGGGGCGACTCGGAGTCGACGTGTTGGATGC 26 47 1 CGGAGTGACG 0.95424 -65 ACGGTACCCACGAGGTGGCTCACGCATTCAG 26 90 0 CGAGGTGCTC 0.942109 -22 ATACAGGGTCCGAGGTGGCCGCCGCCCGCGC 27 26 1 CGAGGTGCCG 0.971225 -211 CTTAACTTGGCCAGGTTGCCCGCGGTGTCGA 27 136 1 CCAGGTGCCC 0.90486 -101 CATCGACGAGCGGGGTTGCCGA 27 225 1 CGGGGTGCCG 0.985759 -12 ****** **** Masking position 6 Map Score: 13.039 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 844 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 CAGCTGCAATGATATCTTTTTCAGGTATATG 1 31 1 GATTCTTTTT 0.959084 -270 GTATATGATTGTTCTTTTTTTGGCCGGTGAT 1 55 1 GTTTTTTTTT 0.683118 -246 ATCCGGTTACGATGTTTTTTACCCATGTCCC 1 84 1 GATTTTTTTA 0.776049 -217 GATCCTCGAACATTTCTTTTTTCGATATATT 1 187 1 CATTCTTTTT 0.69589 -114 TCGACCGGTTGATCTTTTTTTACCAAAACGG 3 266 1 GATTTTTTTT 0.94434 -35 AGATGAAAGGGGGTTCTTTTTGT 6 44 1 GGGTCTTTTT 0.719617 -13 CTCTTAGAAAGATGTCCTTTTCTTTGCCAT 9 10 0 GATTCCTTTT 0.830177 -121 TTCTAAGAGAGATGTCTTTTTTTATACATAA 9 32 1 GATTCTTTTT 0.959084 -99 ATGTATCAAAGGTTTCATTTTTTTATGTATA 9 54 0 GGTTCATTTT 0.742817 -77 TCGTATAAAAGATATTTTTTTAAATAAAATT 11 96 1 GATTTTTTTT 0.94434 -41 TATAATTCTAGATGTTATTTTACATAGTTCG 12 61 0 GATTTATTTT 0.857794 -202 TTTTTGTTAAGATATTTTTTAGCATAACCGA 15 69 0 GATTTTTTTA 0.776049 -37 AGGAATATAGGAGTTTATTTTTCGCATTATT 21 133 1 GAGTTATTTT 0.655848 -53 *** ******* Masking position 5 Map Score: 9.21442 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 422 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 GATATCTTTTTCAGGTATATGATTGTTCTTTTT 1 41 1 TCATTATGAT 0.885165 -260 TTGAAAGTTTTCATCCTGTTTACCGGTTTTACC 3 110 1 TCACGTTTAC 0.492117 -191 TACTCTTGATTCACCCATATCATAGCATAATAG 3 151 0 TCACTATCAT 0.771278 -150 ATGATAGTTTTCATACTCTTGATTCACCCATAT 3 164 0 TCACCTTGAT 0.872722 -137 TTCCGGTTTATCATACCGATGATAGTTTTCATA 3 182 0 TCACGATGAT 0.961064 -119 GGCGGATGGTTCGACCGGTTGATCTTTTTTTAC 3 256 1 TCGCGTTGAT 0.828747 -45 CGTTATCGGGTCATTTTTATGATTGCTTATGGG 5 31 1 TCATTATGAT 0.885165 -48 CCCTTTCATCTCATGTGTATGATTTGAAAGGAG 6 22 0 TCATTATGAT 0.885165 -35 CATAAAAAAATGAAACCTTTGATACATTTGTTA 9 58 1 TGACTTTGAT 0.555414 -73 AGACAGGCAGTCGCACTCATGACGGAAAAGTGA 10 33 1 TCGCCATGAC 0.6417 -131 AAAAGTGAACTCACTTAGTTGACCTGACTGATG 10 58 1 TCATGTTGAC 0.857982 -106 CACGTTCAAACCTTTCATTGAACAAAAT 15 6 1 TCACTTTCAT 0.725856 -100 AAATCAGGTGGATGAAAGCCGGCGCC 16 4 1 TCATGATGAA 0.543445 -87 TTCTCCTTTTTCAAACGTATGATTGGTTTTATC 18 43 0 TCACTATGAT 0.953073 -27 TGATGTAATGTCAATTCTTTGACGAATCGATTT 22 54 1 TCATTTTGAC 0.832521 -101 GCGGTCGACCTCACCCAGATGACT 25 2 0 TCACGATGAC 0.952992 -299 *** * ****** Masking position 10 Map Score: 8.66791 Number of sites scoring better than the average of aligned sites = 800 Number in coding regions = 748 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TAACCGCAGGAAGGAGGGGTGGGACATGGG 1 105 0 AAGGAGGGGT 0.972735 -196 ACCATAGGGAAAGGATCGATTAGGACATGG 3 51 1 AAGGATCGAT 0.948758 -250 TTATAAAAGGAAGGAGGGATACACCGCCC 9 112 1 AAGGAGGGAT 0.981487 -19 CTTAATCGAAAAGGATCGGTGACCAAAC 13 12 1 AAGGATCGGT 0.925714 -18 AAATAGAAAAGGCGGGAAAATCAA 20 9 1 AAGGCGGGAA 0.930033 -16 CAGCCTTTAGAAGGCTGGATTTTTTA 22 7 0 AAGGCTGGAT 0.981487 -148 CAGCCTTCTAAAGGCTGGATCTTTTCGTTT 22 20 1 AAGGCTGGAT 0.981487 -135 ********** Masking position 2 Map Score: 6.81171 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 62 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 CTTTTTTTGGCCGGTGATCCGGTTACGATGTTT 1 68 1 CGTATCCGGT 0.987799 -233 CTCAGAAAAACGGATAATCGGGGTGTTAATTTG 1 141 0 CGTATCGGGG 0.987555 -160 ACTTTTACAGCGGAGCTTCCGGTTTATCATACC 3 198 0 CGGTTCCGGT 0.942788 -103 GACCCGATCGCCCGTTATCGGGTCATTTTTATG 5 19 1 CCTATCGGGT 0.966148 -60 ATGTCAGGCCCAGCTGATCCGGTCACTACATGT 25 101 0 CGTATCCGGT 0.987802 -200 GGGAAACCTTCTGATCGTCGGGTCGGTTGTCGG 25 146 0 CGTGTCGGGT 0.961417 -155 CCACCTCGGACCCTGTATCGGGGAGATCCCGGT 27 11 0 CCGATCGGGG 0.955797 -226 TCGGGATCGTGTGTGGATCCGGGGTTAGGCTGG 27 176 1 GGGATCCGGG 0.927938 -61 * * * ******* Masking position 8 Map Score: 4.54027 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 55 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 GCTGAAGTTTGTTTCATCATGACATTCGTT 1 232 1 GTTTCATCAT 0.94638 -69 CGGAGCTTCCGGTTTATCATACCGATGATA 3 191 0 GGTTTATCAT 0.833319 -110 TACAATTACTGTTTCCTCAGAAAACGGAAA 14 68 0 GTTTCCTCAG 0.923126 -48 ATCAAAAGCAGTTTTATCAGGACTGATCCA 16 57 1 GTTTTATCAG 0.94638 -34 CGTATGATTGGTTTTATCATATCATCTGAA 18 31 0 GTTTTATCAT 0.955353 -39 GGTTTTCTCCTTTTTCAAACG 18 59 0 GTTTTCTCCT 0.804831 -11 ATCAATGCCGTTCCCTCATGGTCACGCAA 21 10 1 GTTCCCTCAT 0.772802 -176 GGCGATACTCCTTTTATCATGTTTTTAGGC 21 166 0 CTTTTATCAT 0.756637 -20 GAACGAATTGGTTTTATCAGCATAACGAAA 22 90 0 GTTTTATCAG 0.94638 -65 ********** Masking position 7 Map Score: 4.69742 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 192 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 TAGAACAAAGCGGTAAAACCGGTAAACAGG 3 124 0 CGGTAAAACC 0.900811 -177 GGGCGGTGTATCCCTCCTTCCTT 9 118 0 CGGTGTATCC 0.880841 -13 TTCGGATTAAAGGGGAATTCAA 12 3 0 AGGGGAATTC 0.896966 -260 GACATATGTGAGGTGAAACCGC 12 251 1 AGGTGAAACC 0.911855 -12 CAACTCTATTCGGTGATTTCAGATGATATG 18 14 1 CGGTGATTTC 0.86546 -56 ATAGAAAAGGCGGGAAAATCAA 20 13 1 CGGGAAAATC 0.884294 -12 GTCTCCTTGTGGGTGAATTCCTTATAACTT 24 18 1 GGGTGAATTC 0.87103 -70 CGCGACTTGCCGGGGAAACCTTCTGATCGT 25 161 0 CGGGGAAACC 0.982734 -140 GACCCTGTATCGGGGAGATCCCGGT 27 6 0 CGGGGAGATC 0.911734 -231 GGTTTGCCAGCGGTGAATACAACGGCGACA 27 65 0 CGGTGAATAC 0.909642 -172 ********** Masking position 10 Map Score: 4.61984 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 386 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 TTGAAAACCTAACCGCAGGAAGGAGGGGTG 1 114 0 AACCGCAGGA 0.823147 -187 TAAACAAAAAAGCCGCAGCCACCTGCGG 2 9 0 AGCCGCAGCC 0.949208 -152 GGTGGATGAAAGCCGGCGCCAGCCTGTATA 16 17 1 AGCCGGCGCC 0.878917 -74 GGGTGAGGTCGACCGCAGGCTGATCCAGCC 25 19 1 GACCGCAGGC 0.975358 -282 CGCTGTTGGCCAGCGCGGCCGATCGGCTGG 25 43 0 CAGCGCGGCC 0.920107 -258 GGTCCGAGGTGGCCGCCGCCCGCGCGAGAC 27 32 1 GGCCGCCGCC 0.644739 -205 CCGTTGTATTCACCGCTGGCAAACCCCTTA 27 70 1 CACCGCTGGC 0.962804 -167 GACTGTTCGACACCGCGGGCAACCTGGCCA 27 143 0 CACCGCGGGC 0.982735 -94 ********** Masking position 5 Map Score: 3.26871 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 746 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 CCTCCCTGTGGATCAGTCCTGATAAAACTG 16 65 0 GATCAGTCCT 0.964454 -26 TTGATCAGTCCCCTTTTCAATT 22 143 0 GATCAGTCCC 0.986668 -12 GTGATCAGTCTCCTTGTGGGTG 24 3 1 GATCAGTCTC 0.970454 -85 CGATCGGCTGGATCAGCCTGCGGTCGACCT 25 24 0 GATCAGCCTG 0.936695 -277 CCGCGGTGTCGAACAGTCCGATCGGGATCG 27 155 1 GAACAGTCCG 0.957436 -82 ********** Masking position 5 Map Score: 1.21167 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 47 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 TTCTTACATTTATTTTACATTTTTAGAAAT 4 21 1 TATTTTACAT 0.940605 -98 TATCACTTTATATTTTACATAATCGCGCGC 4 65 0 TATTTTACAT 0.940605 -54 AGATGTCTTTTTTTATACATAAAAAAATGA 9 41 1 TTTTATACAT 0.796194 -90 TTCTAGATGTTATTTTACATAGTTCGTATT 12 57 0 TATTTTACAT 0.940605 -206 GATTTGCTTTTATTATACAGGCTGGCGCCG 16 30 0 TATTATACAG 0.852736 -61 TTCAGATTAATATCATACATATTGTGAACG 22 115 0 TATCATACAT 0.852737 -40 ********** Masking position 6 Map Score: 0.94533 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 16 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 14 CGGTTAGGTTTTCAAATTAACACCCCGATT 1 129 1 TTCAAATTAA 0.68564 -172 TATCATACTCTTCGGATTAAAGGGGAATTC 12 13 0 TTCGGATTAA 0.818116 -250 AATTTGTGTTTTCAGGCTAAATTGTAGGTT 12 130 0 TTCAGGCTAA 0.934335 -133 TGTCAATGAGTTAAGATTAATTTTTTCTAT 21 56 0 TTAAGATTAA 0.62005 -130 TTTTGATTTATTCATATTAAACGACTAGGA 21 107 1 TTCATATTAA 0.681075 -79 TTTCGCATTATTCAGCCTAAAAACATGATA 21 152 1 TTCAGCCTAA 0.881636 -34 CCCTTTTCAATTCAGATTAATATCATACAT 22 125 0 TTCAGATTAA 0.949269 -30 TCATGTCGTTTTCAGGCTATAGTCCCA 23 8 0 TTCAGGCTAT 0.818333 -32 GGCTCACGCATTCAGACTATGCGGTTTGCA 26 75 0 TTCAGACTAT 0.888315 -37 ********** Masking position 8 Map Score: 1.58819 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 79 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 15 AAAAACGGATAATCGGGGTGTTAATTTGAA 1 139 0 AATCGGGGTG 0.688216 -162 TCGGTATGATAAACCGGAAGCTCCGCTGTA 3 196 1 AAACCGGAAG 0.797768 -105 TTTTTTACCAAAACGGGGAGTAGATCAAGA 3 281 1 AAACGGGGAG 0.961728 -20 ATAGAAACGAGGAGAAGTTAT 8 5 1 AAACGAGGAG 0.958667 -17 ACTTAATCGAAAAGGATCGGTGAC 13 5 1 AATCGAAAAG 0.848534 -25 TTTCCTCAGAAAACGGAAAGCAGTCTGCCT 14 57 0 AAACGGAAAG 0.950512 -59 TTTTCTATTCAAGCGAAAAGACCCTTGCGT 21 34 0 AAGCGAAAAG 0.824828 -152 TATTCATATTAAACGACTAGGAATATAGGA 21 115 1 AAACGACTAG 0.753163 -71 ACATCAAATAAAACGAAAAGATCCAGCCTT 22 30 0 AAACGAAAAG 0.946604 -125 TATAGCCTGAAAACGACATGAAGGAGATGC 23 17 1 AAACGACATG 0.803363 -23 ********** Masking position 2 Map Score: 2.87266 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 420 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826